Team:SJTU-Software/Project/Tutorial

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Tutorial

“Easy BBK(An Easy Biobrick Blueprint's pacKage)" has four main function: "search", "compare", "present", and "upload". This part will guide users about how to use this software tool.



2.2.1 How to start EASY BBK

Software environment: Java SE Development Kit 6 and later version.
1. Download EASY BBK from github
2. Download the latest JDK from http://www.oracle.com/technetwork/java/javase/downloads/index.html

3. Double click the Easybbk.jar and start Easybbk



2.2.2 Home Page

1/2. Click each icon to enter each function

2.2.3 Search

1. Go back to home page
2. Input keyword or sequence
3. Search by keyword
4. Search by sequence
5. Display advanced search conditions

1. Adjust the weight of the 4 properties to make them add up to 100
2. Click “Confirm” before starting search by keyword or sequence

1. Forward or Back to previous or next page
2. Display detail information of the biobrick
3. Click to view the main page of the biobrick on iGEM Registry
4. Check to add the biobrick to “compare”
5. Click to view the result most related to the biobrick on Google Scholar
6. Go to the previous page of search results
7. Go to the next page of search results
8. After biobricks being added from “search”, click to go to “compare” the biobricks


2.2.4 Compare

1. Remove the biobrick below from “Compare”
2. Click to view the main page of the biobrick on iGEM Registry
3. After biobricks being viewed in “compare”, click to go back to “search” results

2.2.5 Present

2.2.5.1 General introduction of Present Page

1. Basic Functions
2. Backbone
3. Components on backbone
4. Proteins, plasmid, virus and bacteria
5. Relation between biobricks
6. Style settings of lines above
7. Bio-system drawing panel
8. Status bar

Basic Functions

1. Discard previous work and create a new bio-system
2. Open previously saved XML file
3. Save the drawn bio-system as an XML file to further edit next time
4. Export the picture of the bio-system as .jpg, .bmp or .png file.
5. Add text to the drawing panel
6. Change the font, size and color of the text
7. Delete components on drawing panel
8. Undo
9. Redo

Components on in bio-systems

1. Promoter
2. Ribosome binding site (RBS)
3. Protein coding sequence
4. Terminator
5. Primer
6. Reporter
7. Protein 1
8. Protein 2
9. Combined protein
10. Plasmid
11. Virus
12. Bacteria

Relation and backbone in bio-systems

1. Inhibit
2. Enhance
3. Other relations (e.g. this could denote a coding sequence code a protein.)
4. Backbone
5. Style settings of lines above

2.2.5.2 Start presenting your bio-system

1st: Draw backbone

Step 1. Click the "Backbone" icon
Step 2. Click anywhere on drawing panel to add a "Backbone"
Step 3. Stretch the "Backbone"
Step 4. Drag the "Backbone" to anywhere on drawing panel

2nd: Add a component to backbone

Step 1. Click the "Promoter" icon
Step 2. Click anywhere on drawing panel to add a "Promoter"
Step 3. Drag the "Promote" near "Backbone"
Step 4. Release the mouth to make the "Promoter" automatically become part of the sequence

3rd: Adjust the position of the components or backbones already existing on the drawing panel

1. Drag the "Protein Coding Sequence" to a suitable position
2. Stretch the "Backbone" to a suitable length
3. Drag the "Backbone" to anywhere on drawing panel

4th: Add proteins to bio-system

Step 1. Click the "Protein 2" icon
Step 2. Click anywhere on drawing panel to add proteins

5th: Draw a relation between components

Step 1. Click the "Inhibit" icon
Step 2. Click here
Step 3. Click here
Step 4. Click here (More clicks could be done until you get your desired shape of this relation.)

6th: Add text to drawing panel

Step 1. Click the “Text” icon
Step 2. Click anywhere on drawing panel to add text
Step 3. Click to change the font, size and color of the text

7th: Delete a component on drawing panel

Step 1. Click this icon
Step 2. Click any component on drawing panel to delete it

8th: Set the detail of the component on drawing panel

Step 1. Double click any component on backbone
Step 2. Input a part name
Step 3. Click “Set” to search this part out from database
Step 4. Click “OK” to set the detail of the component

9th: Upload the presented biobrick

By setting the detail on all the biobricks on a single backbone, user can choose to upload the biobrick to Registry or Easy BBK database. The upload form will be automatically filled out.
Step 1. Double click the backbone of the biobrick
Step 2. Click "OK" to confirm to upload the biobrick
Step 3. Go to "upload" to check the filled out form

10th: On finishing presenting the bio-system (Using 2013 Buenos Aires as example)

Step 1. Save the drawn bio-system as an XML file to further edit next time
Step 2. Export the picture of the bio-system as .jpg, .bmp or .png file.
Step 3. Open previously saved XML file continue drawing



2.2.6 Upload

1. Input information of biobrick

1. Input iGEM user name and password
2. Click to submit the biobrick to Easy BBK database
3. Click to submit the biobrick to Registry



iGemdry2014@163.com

SJTU-Software,Shanghai,China

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